Publications

  1. Zhang, X; Shi, X.\(^\ast\); Liu, Y.; Liu, X.; Ma, S. (2023) A General Framework for Identifying Hierarchical Interactions and Its Application to Genomics Data, \(\underline{Journal \space of \space Comput \space \& \space Graph \space Statist}\), R package

  2. Liu W.; Liao X; Luo Z.; Yang Y.; Lau M.; Jiao Y.; Shi X.; Zhai W.; Ji H.; Yeong J.; Liu J. (2023) Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST, \(\underline{Nature \space Communications}\), doi: 10.1038/s41467-023-35947-w, R package

  3. Liu, Wei; Liao, Xu; Yang, Yi; Lin, Huazhen; Yeong, Joe; Zhou, Xiang\(^\ast\); Shi, Xingjie\(^\ast\); Jin Liu\(^\ast\): Joint dimension reduction and clustering analysis of single-cell RNA-seq and spatial transcriptomics data, \(\underline{Nucleic \space Acids \space Research}\), 2022, gkac219, R Package

  4. Zhang, Xiao; Liu, Xu; Shi, Xingjie\(^\ast\); Model Selection for Varying Coefficient Nonparametric Transformation Model, \(\underline{Econometric \space Journal}\), accepted, R Package

  5. Yang, Yi\(^\#\); Shi, Xingjie\(^\#\); Zhou, Qiuzhong; Sun, Lei; Yeong, Joe\(^\ast\); Liu, Jin\(^\ast\); SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes, \(\underline{Briefings \space in \space Bioinformatics}\), 2022, 23(1): bbab466, R package,

  6. Cheng, Qing; Qiu, Tingting; Chai, Xiaoran; Sun, Baoluo; Xia, Yingcun; Shi, Xingjie\(^\ast\); Liu, Jin\(^\ast\); MR-Corr\(^2\): A two-sample Mendelian randomization method that accounts for correlated horizontal pleiotropy using correlated instrumental variants, \(\underline{Bioinformatics}\), 2022, 38(2): 303-310, R Package

  7. Shi, Xingjie; Chai, Xiaoran; Yang, Yi; Cheng, Qing; Jiao, Yuling; Chen, Haoyue; Huang, Jian; Yang, Can; Liu, Jin\(^\ast\); A tissue-specific collaborative mixed model for jointly analyzing multiple tissues in transcriptome-wide association studies, \(\underline{Nucleic \space Acids \space Research}\), 2020, 48(19): e109. R Package.

  8. Shi, Xingjie; Ma, Shuangge; Huang, Yuan\(^\ast\); Promoting sign consistency in the cure model estimation and selection, \(\underline{Statistical \space Methods \space in \space Medical \space Research}\), 2020, 29(1): 15-28. Software.

  9. 史兴杰; 王赛旎 & 李扬 ; 高维数据的稳健二分类方法, \(\underline{统计研究}\), 2020, 37(9): 95-105.

  10. Cheng, Qing; Yang, Yi; Shi, Xingjie; Yeung, Kar-Fu; Yang, Can; Peng, Heng; Liu, Jin; MR-LDP: A two-sample Mendelian randomization for GWAS summary statistics accounting for linkage disequilibrium and horizontal pleiotropy, \(\underline{NAR \space Genomics \space and \space Bioinformatics}\), 2020, 2(2): lqaa028. R Package

  11. Shi, Xingjie; Jiao, Yuling; Yang, Yi; Cheng, Ching-Yu; Yang, Can; Lin, Xinyi\(^\ast\); Liu, Jin\(^\ast\); VIMCO: variational inference for multiple correlated outcomes in genome-wide association studies, \(\underline{Bioinformatics}\), 2019, 35(19): 3693-3700. R Package.

  12. 孙怡凡; 吴梦云 & 史兴杰 ; 高维大数据基因网络中的社区发现–以NC方法为例, \(\underline{统计研究}\), 2019, 36(3), 124-128.

  13. Wang, Shuaichao; Shi, Xingjie; Wu, Mengyun; Ma, Shuangge; Horizontal and vertical integrative analysis methods for mental disorders omics data, \(\underline{Scientific \space Reports}\), 2019, 9: 13430.

  14. Yang, Yi; Shi, Xingjie; Jiao, Yuling; Huang, Jian; Chen, Min; Zhou, Xiang; Sun, Lei; Lin, Xinyi; Yang, Can; Liu, Jin; CoMM-S\(^2\): A collaborative mixed model using summary statistics in transcriptome-wide association studies, \(\underline{Bioinformatics}\), 2019, 41(8): 779-789. R Package

  15. Shi, Xingjie; Huang, Yuan; Huang, Jian; Ma, Shuangge; A Forward and Backward Stagewise Algorithm for Nonconvex Loss Functions with Adaptive Lasso, \(\underline{Computational \space Statistics \space and \space Data \space Analysis}\), 2018, 124: 235-251. R Package.

  16. Chai, Hao\(^\#\); Shi, Xingjie\(^\#\); Zhang, Qingzhao; Zhao, Qing; Huang, Yuan; Ma, Shuangge; Analysis of cancer gene expression data with an assisted robust marker identification approach, \(\underline{Genetic \space Epidemiology}\), 2017, 41(8): 779-789.

  17. Jiang, Yu\(^\#\); Shi, Xingjie\(^\#\); Zhao, Qing; Michael. Krauthammer; Bonnie E.Gould Rothberg; Ma, Shuangge; Integrated analysis of multidimensional omics data on cutaneous melanoma prognosis, \(\underline{Genomics}\), 2016, 107(6): 223-30.

  18. Liu, Jin; Yang, Can; Shi, Xingjie; Li, Cong; Huang, Jian; Zhao, Hongyu; Ma, Shuangge; Analyzing Association Mapping in Pedigree-Based GWAS Using a Penalized Multitrait Mixed Model, \(\underline{Genetic \space Epidemiology}\), 2016, 40(5): 382-393.

  19. Shi, Xingjie; Zhao, Qing; Huang, Jian; Xie, Yang; Ma, Shuangge; Deciphering the association between gene expression and copy number alteration using a sparse double Laplacian shrinkage approach, \(\underline{Bioinformatics}\), 2015, 31(24): 3977-3983.

  20. Zhao, Qing; Shi, Xingjie; Huang, Jian; Liu, Jin; Li, Yang; Ma, Shuangge; Integrative analysis of “-omics” data using penalty functions, \(\underline{WIREs \space Computational \space Statistics}\), 2015, 7(1): 99-108.

  21. Shi, Xingjie\(^\#\); Yi, Huangdi\(^\#\); Ma, Shuangge; Measures for the degree of overlap of gene signatures and applications to TCGA, \(\underline{Briefings \space in \space Bioinformatics}\), 2015, 16(5): 735-744.

  22. Wu, Cen; Shi, Xingjie; Cui, Yuehua; Ma, Shuangge; A penalized robust semiparametric approach for gene–environment interactions, \(\underline{Statistics \space in \space Medicine}\), 2015, 34 (30): 4016–4030.

  23. Zhao, Qing\(^\#\); Shi, Xingjie\(^\#\); Xie, Yang; Huang, Jian; Shia, Benchang; Ma, Shuangge; Combining Multidimensional Genomic Measurements for Predicting Cancer Prognosis: Observations from TCGA, \(\underline{Briefings \space in \space Bioinformatics}\), 2015, 16(2): 291-303.

  24. Shi, Xingjie; Liu, Jin; Huang, Jian; Zhou, Yong; Shia, Benchang; Ma, Shuangge; Integrative Analysis of Cancer Prognosis Data with Contrasted Group Bridge Penalization, \(\underline{Genetic \space Epidemiology}\), 2014, 38(2): 141-151.

  25. Shi, Xingjie; Liu, Jin; Huang, Jian; Zhou, Yong; Xie, Yang; Ma, Shuangge; A Penalized Robust Method for identifying Gene-Environment Interactions, \(\underline{Genetic \space Epidemiology}\), 2014, 38(3): 220-230.

  26. 史兴杰 & 周勇 ; 房地产泡沫检验的Switching AR模型, \(\underline{系统工程理论与实践}\), 2014, 34(3): 676-682.

  27. Shi, Xingjie; Shen, Shihao; Liu, Jin; Huang, Jian; Zhou, Yong; Ma, Shuangge; Similarity of Markers Identified from Cancer Gene Expression Studies: Observations from GEO, \(\underline{Briefings \space in \space Bioinformatics}\), 2013, 15(5): 671-684.

  28. 刘玉涛; 史兴杰 & 周勇; 左截断右删失数据下光滑分布函数估计效率, \(\underline{数学学报}\), 2013, 56(5): 625-636.